rs3129878

Positions:

• chr6-32440958-A-C
• chr6-32440958-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_019111.5(HLA-DRA):​c.82+926A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 152,126 control chromosomes in the GnomAD database, including 6,913 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.30 (6913 hom., cov: 33)
• Consequence: HLA-DRA NM_019111.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452

Genes affected

HLA-DRA (HGNC:4947): (major histocompatibility complex, class II, DR alpha) HLA-DRA is one of the HLA class II alpha chain paralogues. This class II molecule is a heterodimer consisting of an alpha and a beta chain, both anchored in the membrane. This molecule is expressed on the surface of various antigen presenting cells such as B lymphocytes, dendritic cells, and monocytes/macrophages, and plays a central role in the immune system and response by presenting peptides derived from extracellular proteins, in particular, pathogen-derived peptides to T cells. The alpha chain is approximately 33-35 kDa and its gene contains 5 exons. Exon 1 encodes the leader peptide, exons 2 and 3 encode the two extracellular domains, and exon 4 encodes the transmembrane domain and the cytoplasmic tail. DRA does not have polymorphisms in the peptide binding part and acts as the sole alpha chain for DRB1, DRB3, DRB4 and DRB5. [provided by RefSeq, Aug 2020]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HLA-DRA	NM_019111.5	c.82+926A>C		intron_variant		ENST00000395388.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HLA-DRA	ENST00000395388.7	c.82+926A>C		intron_variant			NM_019111.5	P1
HLA-DRA	ENST00000374982.5	c.82+926A>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.296 AC: 45067 AN: 152006 Hom.: 6910 Cov.: 33

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.312

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.296 AC: 45092 AN: 152126 Hom.: 6913 Cov.: 33 AF XY: 0.300 AC XY: 22294 AN XY: 74352

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.309

Alfa AF: 0.293 Hom.: 9929

Bravo AF: 0.283

Asia WGS AF: 0.314 AC: 1096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.45

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3129878; hg19: chr6-32408735;